Chirally enriched synthetic phosphate oligomers
Oligomers having phosphonate internucleosidyl linkages which are enriched for phosphonate linkages of a preselected chirality which hybridize to an RNA target sequence and methods for their preparation are provided.
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Claims
1. A method of making an Oligomer having phosphonate internucleosidyl linkages which hybridizes to an RNA target sequence, said method comprising the steps of:
- (a) identifying a single stranded RNA target sequence,
- (b) synthesizing a nucleoside dimer, trimer or tetramer having racemic internucleosidyl phosphonate linkages;
- (c) purifying from said racemic nucleoside dimer, trimer or tetramer a chirally pure nucleoside dimer, trimer or tetramer; and
- (d) sequentially linking two or more of said chirally pure nucleoside dimers, trimers or tetramers to form a synthetic Oligomer enriched for phosphonate internucleosidyl linkages of preselected chirality and wherein the Oligomer is complementary to said identified RNA target sequence.
2. A method according to claim 1 wherein greater than 40% of the phosphonate linkages in the Oligomer formed in step d) are chirally pure.
3. A method according to claim 2 wherein said chirally pure phosphonate linkages are Rp lower alkylphosphonate linkages having alkyl groups of 1 to 3 carbon atoms.
4. A method according to claim 3 wherein said Rp lower alkylphosphonate linkages are Rp methylphosphonate linkages.
5. A method of making a Oligomer which hybridizes to an RNA target sequence, said method comprising the steps of:
- (a) identifying a single stranded RNA target sequence; and
- (b) synthesizing an Oligomer having phosphonate internucleosidyl linkages selected from the group consisting of lower alkyl- or arylphosphonate internucleosidyl linkages and lower alkyl- or aryl-phosphonothioate internucleosidyl linkages wherein at least 40% of the phosphonate linkages are chirally pure and wherein the oligomer is complementary to said identified RNA target sequence.
6. A method according to claim 5 wherein the chirally pure phosphonate linkages are interspersed with single racemic phosphonate linkages.
7. A method according to claim 6 wherein said chirally pure phosphonate linkages are interspersed with racemic phosphonate linkages in a ratio of from 1 to about 1 to 1 to about 4 racemic phosphonate linkages to chirally pure phosphonate linkages.
8. A method according to claim 7 wherein said phosphonate linkages are lower alkylphosphonate linkages and said chirally pure linkages are Rp.
9. A method according to claim 8 wherein said lower alkylphosphonate linkages are methylphosphonate linkages.
10. A method according to claim 9 wherein the nucleosides of the oligomer have 2'-O-methyl ribosyl groups as sugar moieties.
11. A method according to claim 5 wherein said synthetic oligomer is synthesized by linking together chirally pure R.sub.p -configuration nucleoside dimers of the formula: ##STR7## wherein X is oxygen or sulfur, R is alkyl of 1 to 3 carbon atoms or aryl, Z is hydrogen, alkoxy of from 1 to 10 carbon atoms, halogen or alkenyloxy of 3 to 6 carbon atoms; B is an independently selected and optionally protected purine or pyrimidine base, B1 is a blocking group and Cp is a coupling group selected from the group consisting of methyl phosphonamidite, methylphosphonmonochloridite, and P(V) methylphosphonate.
12. A method according to claim 7 wherein X is oxygen and R is methyl.
13. A method according to claim 12 wherein the chirally pure phosphonate linkages are Rp.
14. A method according to claim 13 wherein Z is hydrogen.
15. A method according to claim 13 wherein Z is methoxy.
16. A synthetic oligomer, wherein the synthetic oligomer is enriched for R.sub.p -configuration internucleosidyl linkages selected from the group consisting of lower alkyl- or arylphosphonate internucleosidyl linkages and lower alkyl- or arylphosphonothioate internucleosidyl linkages wherein chirally pure phosphonate linkages are interspersed with single racemic phosphonate linkages in a ratio of from 1 to about 1 to 1 to about 4 racemic phosphonate linkages.
17. An oligomer according to claim 16 wherein said phosphonate linkages are methylphosphonate linkages and said chirally pure linkages are Rp.
18. An oligomer according to claim 17 wherein the nucleosides of said oligomer have 2'-O-methyl ribosyl groups as sugar moieties.
19. A composition comprising oligomers having phosphonate internucleosidyl linkages selected from the group consisting of lower alkyl- or arylphosphonate linkages and lower alkyl- or arylphosphonothioate linkages wherein the oligomers have chirally pure phosphonate linkages interspersed between single racemic phosphonate linkages, and an acceptable carrier.
20. A method of preparing an oligomer having phosphonate internucleosidyl linkages which comprises linking together synthons having chirally pure internucleosidyl linkages of the formula: ##STR8## wherein X is oxygen or sulfur, R is alkyl of 1 to 3 carbon atoms or aryl, Z is hydrogen, alkoxy of from 1 to 10 carbon atoms, halogen or alkenyloxy of 3 to 6 carbon atoms; B is an independently selected and optionally protected purine or pyrimidine base, B1 is a blocking group and Cp is a coupling group selected from the group consisting of methyl phosphonamidite, methylphosphonmonochloridite, and P(V) methylphosphonate.
| 5212295 | May 18, 1993 | Cook |
| 0411186 | February 1991 | EPX |
| 9202532 | February 1992 | WOX |
Type: Grant
Filed: Jun 30, 1997
Date of Patent: Sep 21, 1999
Assignee: Genta, Incorporated (San Diego, CA)
Inventors: Lyle John Arnold, Jr. (Poway, CA), Mark Alan Reynolds (San Diego, CA), Timothy Andrew Riley (Nipomo, CA), David Aaron Schwartz (Encinitas, CA), Morteza Monir Vaghefi (San Diego, CA)
Primary Examiner: Marian C. Knode
Assistant Examiner: L. Eric Crane
Law Firm: Knobbe, Martens, Olson & Bear, LLP
Application Number: 8/885,126
International Classification: C07H 2104;
